RetrogeneDB ID:

retro_hsap_4287

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:97049983..97050832(-)
Located in intron of:ENSG00000175787
Retrocopy
information
Ensembl ID:ENSG00000237679
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:VDAC1
Ensembl ID:ENSG00000213585
Aliases:VDAC1, PORIN, VDAC-1
Description:voltage-dependent anion channel 1 [Source:HGNC Symbol;Acc:12669]


Retrocopy-Parental alignment summary:






>retro_hsap_4287
ATGGCTGTGCTACTCACATATGAGATCCTGTCAAATCTGCCAGGGATGTCTTCACCAATGGCTATGGATTTGGCTTAATA
AAGCTTGATTTGAAAACAAAAGAGAAGAATGGATTGGAATTTACAAGCTCAGGCTCAGCCAACACTGAGAATACCAAAGT
GACGGGCAGTCTGGAAACCAAGTACAGATGGACTGAATATGGCCTGGCATTTACAGAGAAATAGAACACCGACAACACAC
CAGGCACTGAGGTTACTGTGGAAGATCAGCTTGCACGTGAACTGAAGCTGACCTTCAATTCGTCCTTCTCACCTAACACT
GGGGGAAAAAAATGCTAAAATCAAGACAGGGTACAAGTAGGAGCACATTAACCTGGGCTGAGACATGGATTTTGACATTG
CTGGGCCCTCATTCCAGGGTGCTCTGGTGCTGGGTTATGAGGGCTGGCTGGCTAGCTACCAGATGAATTTTGAGAATGCA
AAGTCCCGAGTGACCTAGAGCAACAGTGTAGTTGGCTACAAGACTGATGAATTCCAGTTTCACACTAAAGTGAATGATGG
GACAGAGTTTGGCAGCTCCATTTACTAGAAGGTGAACAAGAAGTTGGAGACTGCTGTCAATCTCGCCTGGACAGCAGGAA
ACAGTAACACTAGCTTCGGAATAGCAGCCAAGTATCAGATCGACCCTGACGCCTACTTCTCGGCTAAAATGAACAACTCC
AGCCTGAGAGGTTTAGGATACAATCAAACCCTAAAGCCAGGTATCAAACTGACACTGTCAGCTCTCCTGGATGGCAAGAA
CGTCAATGCTGGTGGCCACAAGCTTGGTTGAGGACTAGAATTTCAAGCA

ORF - retro_hsap_4287 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.02 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAVPPTYADLG-KSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGL
MAV..TY..L..KSARDVFT.GYGFGLIKLDLKTK..NGLEFTSSGSANTE.TKVTGSLETKYRWTEYGL
RetrocopyMAVLLTYEILS<KSARDVFTNGYGFGLIKLDLKTKEKNGLEFTSSGSANTENTKVTGSLETKYRWTEYGL
ParentalTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTG-KKNAKIKTGYKREHINLGCDMDFDIAGPSI
.FTEK.NTDNT.GTE.TVEDQLAR.LKLTF.SSFSPNTG..KNAKIKTGYK.EHINLG.DMDFDIAGPS.
RetrocopyAFTEK*NTDNTPGTEVTVEDQLARELKLTFNSSFSPNTG>EKNAKIKTGYK*EHINLG*DMDFDIAGPSF
ParentalRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNL
.GALVLGYEGWLA.YQMNFE.AKSRVT.SN..VGYKTDEFQ.HT.VNDGTEFG.SIY.KVNKKLETAVNL
RetrocopyQGALVLGYEGWLASYQMNFENAKSRVT*SNSVVGYKTDEFQFHTKVNDGTEFGSSIY*KVNKKLETAVNL
ParentalAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLG
AWTAGNSNT.FGIAAKYQIDPDA.FSAK.NNSSL.GLGY.QTLKPGIKLTLSALLDGKNVNAGGHKLG.G
RetrocopyAWTAGNSNTSFGIAAKYQIDPDAYFSAKMNNSSLRGLGYNQTLKPGIKLTLSALLDGKNVNAGGHKLG*G
ParentalLEFQA
LEFQA
RetrocopyLEFQA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .06 RPM 139 .03 RPM
bodymap2_adrenal 0 .14 RPM 107 .87 RPM
bodymap2_brain 0 .12 RPM 238 .15 RPM
bodymap2_breast 0 .10 RPM 187 .24 RPM
bodymap2_colon 0 .00 RPM 146 .99 RPM
bodymap2_heart 0 .00 RPM 396 .10 RPM
bodymap2_kidney 0 .00 RPM 255 .40 RPM
bodymap2_liver 0 .00 RPM 168 .10 RPM
bodymap2_lung 0 .00 RPM 101 .88 RPM
bodymap2_lymph_node 0 .00 RPM 109 .48 RPM
bodymap2_ovary 0 .00 RPM 134 .92 RPM
bodymap2_prostate 0 .00 RPM 109 .60 RPM
bodymap2_skeletal_muscle 0 .00 RPM 566 .19 RPM
bodymap2_testis 0 .00 RPM 106 .24 RPM
bodymap2_thyroid 0 .00 RPM 217 .29 RPM
bodymap2_white_blood_cells 0 .00 RPM 86 .27 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4287 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4287 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4287 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4287 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4287 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2905
Parental genes homology:
Parental genes homology involve 27 parental genes, and 105 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009851 retrocopy
retro_cfam_1728,
Choloepus hoffmanni ENSCHOG000000056316 retrocopies
retro_chof_1774, retro_chof_2420, retro_chof_813, retro_chof_858, retro_chof_866, retro_chof_99,
Callithrix jacchus ENSCJAG000000135568 retrocopies
retro_cjac_1216, retro_cjac_1669, retro_cjac_1728, retro_cjac_2677, retro_cjac_3183, retro_cjac_3864, retro_cjac_454, retro_cjac_907,
Cavia porcellus ENSCPOG000000238402 retrocopies
retro_cpor_1061, retro_cpor_699,
Dasypus novemcinctus ENSDNOG000000026805 retrocopies
retro_dnov_1367, retro_dnov_2117, retro_dnov_271, retro_dnov_30, retro_dnov_90,
Dipodomys ordii ENSDORG000000007141 retrocopy
retro_dord_636,
Equus caballus ENSECAG000000123652 retrocopies
retro_ecab_831, retro_ecab_832,
Felis catus ENSFCAG000000084211 retrocopy
retro_fcat_1592,
Homo sapiens ENSG000000786681 retrocopy
retro_hsap_1375,
Homo sapiens ENSG000001656371 retrocopy
retro_hsap_2114,
Homo sapiens ENSG00000213585 13 retrocopies
retro_hsap_1119, retro_hsap_1250, retro_hsap_2250, retro_hsap_2805, retro_hsap_308, retro_hsap_3527, retro_hsap_4287 , retro_hsap_458, retro_hsap_4721, retro_hsap_4831, retro_hsap_4872, retro_hsap_4930, retro_hsap_847,
Gorilla gorilla ENSGGOG000000108803 retrocopies
retro_ggor_693, retro_ggor_875, retro_ggor_981,
Loxodonta africana ENSLAFG000000288181 retrocopy
retro_lafr_161,
Macaca mulatta ENSMMUG000000162356 retrocopies
retro_mmul_1023, retro_mmul_1070, retro_mmul_1305, retro_mmul_1851, retro_mmul_2417, retro_mmul_2613,
Monodelphis domestica ENSMODG000000141571 retrocopy
retro_mdom_1120,
Mustela putorius furoENSMPUG000000102201 retrocopy
retro_mputfur_83,
Mus musculus ENSMUSG000000204023 retrocopies
retro_mmus_2013, retro_mmus_3079, retro_mmus_3124,
Nomascus leucogenys ENSNLEG0000000802311 retrocopies
retro_nleu_1044, retro_nleu_1318, retro_nleu_1561, retro_nleu_189, retro_nleu_1991, retro_nleu_2707, retro_nleu_3019, retro_nleu_433, retro_nleu_492, retro_nleu_873, retro_nleu_880,
Otolemur garnettii ENSOGAG000000307422 retrocopies
retro_ogar_1197, retro_ogar_2876,
Ochotona princeps ENSOPRG000000066052 retrocopies
retro_opri_397, retro_opri_467,
Pongo abelii ENSPPYG000000157816 retrocopies
retro_pabe_1042, retro_pabe_1733, retro_pabe_273, retro_pabe_2913, retro_pabe_3756, retro_pabe_700,
Pan troglodytes ENSPTRG0000001723512 retrocopies
retro_ptro_1593, retro_ptro_1900, retro_ptro_249, retro_ptro_2905, retro_ptro_3138, retro_ptro_3215, retro_ptro_3246, retro_ptro_345, retro_ptro_588, retro_ptro_682, retro_ptro_84, retro_ptro_861,
Rattus norvegicus ENSRNOG000000063758 retrocopies
retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947,
Sus scrofa ENSSSCG000000142962 retrocopies
retro_sscr_346, retro_sscr_801,
Ictidomys tridecemlineatus ENSSTOG000000077643 retrocopies
retro_itri_1137, retro_itri_1506, retro_itri_693,
Tursiops truncatus ENSTTRG000000168562 retrocopies
retro_ttru_1347, retro_ttru_752,
Vicugna pacos ENSVPAG000000104481 retrocopy
retro_vpac_38,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.16 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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